ソフトウェア | 名称 | バージョン | 分類 |
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REFMAC | 5.8.0267精密化 | xia2 | | データ削減 | Aimless | | データスケーリング | PHASER | | 位相決定 | |
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精密化 | 構造決定の手法: 分子置換 開始モデル: 4bbw 解像度: 1.92→77.634 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.882 / SU B: 19.933 / SU ML: 0.268 / 交差検証法: FREE R-VALUE / ESU R: 0.268 / ESU R Free: 0.224 / 詳細: Hydrogens have been added in their riding positions
| Rfactor | 反射数 | %反射 |
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Rfree | 0.3457 | 4147 | 5.015 % |
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Rwork | 0.3128 | 78537 | - |
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all | 0.315 | - | - |
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obs | - | 82684 | 95.144 % |
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溶媒の処理 | イオンプローブ半径: 0.7 Å / 減衰半径: 0.7 Å / VDWプローブ半径: 1 Å / 溶媒モデル: MASK BULK SOLVENT |
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原子変位パラメータ | Biso mean: 41.123 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.343 Å2 | -0 Å2 | -0 Å2 |
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2- | - | -0.343 Å2 | -0 Å2 |
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3- | - | - | 0.685 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.92→77.634 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 8046 | 0 | 40 | 300 | 8386 |
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拘束条件 | Refine-ID | タイプ | Dev ideal | Dev ideal target | 数 |
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X-RAY DIFFRACTION | r_bond_refined_d0.005 | 0.013 | 8242 | X-RAY DIFFRACTION | r_bond_other_d0.001 | 0.014 | 7801 | X-RAY DIFFRACTION | r_angle_refined_deg1.318 | 1.643 | 11193 | X-RAY DIFFRACTION | r_angle_other_deg1.169 | 1.58 | 17918 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg7.762 | 5 | 1036 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg33.179 | 21.111 | 441 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg13.053 | 15 | 1396 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg15.913 | 15 | 72 | X-RAY DIFFRACTION | r_chiral_restr0.051 | 0.2 | 1118 | X-RAY DIFFRACTION | r_gen_planes_refined0.004 | 0.02 | 9362 | X-RAY DIFFRACTION | r_gen_planes_other0.001 | 0.02 | 1914 | X-RAY DIFFRACTION | r_nbd_refined0.18 | 0.2 | 1375 | X-RAY DIFFRACTION | r_symmetry_nbd_other0.183 | 0.2 | 7804 | X-RAY DIFFRACTION | r_nbtor_refined0.147 | 0.2 | 3847 | X-RAY DIFFRACTION | r_symmetry_nbtor_other0.071 | 0.2 | 3948 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.147 | 0.2 | 371 | X-RAY DIFFRACTION | r_symmetry_nbd_refined0.092 | 0.2 | 7 | X-RAY DIFFRACTION | r_nbd_other0.162 | 0.2 | 38 | X-RAY DIFFRACTION | r_symmetry_xyhbond_nbd_refined0.07 | 0.2 | 2 | X-RAY DIFFRACTION | r_mcbond_it0.649 | 1.546 | 4150 | X-RAY DIFFRACTION | r_mcbond_other0.649 | 1.545 | 4149 | X-RAY DIFFRACTION | r_mcangle_it1.162 | 2.315 | 5184 | X-RAY DIFFRACTION | r_mcangle_other1.162 | 2.316 | 5185 | X-RAY DIFFRACTION | r_scbond_it0.476 | 1.603 | 4092 | X-RAY DIFFRACTION | r_scbond_other0.476 | 1.603 | 4093 | X-RAY DIFFRACTION | r_scangle_it0.871 | 2.381 | 6009 | X-RAY DIFFRACTION | r_scangle_other0.871 | 2.381 | 6010 | X-RAY DIFFRACTION | r_lrange_it3.974 | 17.774 | 8680 | X-RAY DIFFRACTION | r_lrange_other3.954 | 17.665 | 8648 | X-RAY DIFFRACTION | r_ncsr_local_group_10.08 | 0.05 | 16669 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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Refine LS restraints NCS | Ens-ID | Dom-ID | Auth asym-ID | Refine-ID | タイプ | Rms dev position (Å) | Weight position |
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1 | 1 | AX-RAY DIFFRACTION | Local ncs0.08036 | 0.05009 | 1 | 2 | BX-RAY DIFFRACTION | Local ncs0.08036 | 0.05009 | | | | |
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LS精密化 シェル | 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
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1.92-1.97 | 0.513 | 264 | 0.47 | 5055 | X-RAY DIFFRACTION | 84.3349 | 1.97-2.024 | 0.456 | 290 | 0.414 | 5813 | X-RAY DIFFRACTION | 98.9462 | 2.024-2.082 | 0.46 | 295 | 0.435 | 5608 | X-RAY DIFFRACTION | 98.3178 | 2.082-2.146 | 0.404 | 296 | 0.387 | 5456 | X-RAY DIFFRACTION | 98.7298 | 2.146-2.217 | 0.381 | 282 | 0.376 | 5299 | X-RAY DIFFRACTION | 98.989 | 2.217-2.295 | 0.68 | 193 | 0.674 | 3712 | X-RAY DIFFRACTION | 71.1942 | 2.295-2.381 | 0.387 | 241 | 0.362 | 4957 | X-RAY DIFFRACTION | 98.4656 | 2.381-2.478 | 0.394 | 265 | 0.343 | 4744 | X-RAY DIFFRACTION | 98.0811 | 2.478-2.589 | 0.362 | 266 | 0.33 | 4541 | X-RAY DIFFRACTION | 98.1421 | 2.589-2.715 | 0.366 | 217 | 0.341 | 4358 | X-RAY DIFFRACTION | 97.5272 | 2.715-2.862 | 0.408 | 210 | 0.332 | 4209 | X-RAY DIFFRACTION | 97.7222 | 2.862-3.035 | 0.356 | 211 | 0.308 | 3907 | X-RAY DIFFRACTION | 97.3062 | 3.035-3.245 | 0.36 | 188 | 0.295 | 3706 | X-RAY DIFFRACTION | 97.277 | 3.245-3.505 | 0.317 | 186 | 0.284 | 3470 | X-RAY DIFFRACTION | 97.234 | 3.505-3.84 | 0.343 | 168 | 0.299 | 3092 | X-RAY DIFFRACTION | 93.894 | 3.84-4.293 | 0.296 | 142 | 0.244 | 2901 | X-RAY DIFFRACTION | 96.389 | 4.293-4.957 | 0.212 | 144 | 0.201 | 2628 | X-RAY DIFFRACTION | 97.5369 | 4.957-6.07 | 0.242 | 131 | 0.2 | 2217 | X-RAY DIFFRACTION | 97.105 | 6.07-8.583 | 0.243 | 92 | 0.193 | 1789 | X-RAY DIFFRACTION | 97.7651 | 8.583-77.634 | 0.199 | 66 | 0.217 | 1075 | X-RAY DIFFRACTION | 97.4381 |
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精密化 TLS | 手法: refined / Refine-ID: X-RAY DIFFRACTION ID | L11 (°2) | L12 (°2) | L13 (°2) | L22 (°2) | L23 (°2) | L33 (°2) | S11 (Å °) | S12 (Å °) | S13 (Å °) | S21 (Å °) | S22 (Å °) | S23 (Å °) | S31 (Å °) | S32 (Å °) | S33 (Å °) | T11 (Å2) | T12 (Å2) | T13 (Å2) | T22 (Å2) | T23 (Å2) | T33 (Å2) | Origin x (Å) | Origin y (Å) | Origin z (Å) |
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1 | 0.1109 | -0.1395 | -0.2309 | 0.3966 | 0.7128 | 1.3184 | -0.1837 | -0.0009 | 0.0237 | 0.0845 | 0.0579 | 0.0965 | 0.0491 | 0.2062 | 0.1258 | 0.4523 | -0.0488 | -0.0224 | 0.262 | -0.0219 | 0.1302 | 0.7519 | 16.0308 | 34.2282 | 2 | 0.3734 | -0.0253 | -0.1897 | 0.4936 | 0.15 | 0.3252 | -0.0792 | -0.0022 | 0.0498 | 0.2096 | -0.0059 | 0.0509 | 0.2769 | 0.2814 | 0.0851 | 0.4111 | 0.1854 | 0.0342 | 0.4605 | 0.1205 | 0.0497 | 18.9443 | -17.1296 | 13.2282 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | ALLA34 - 552 | 2 | X-RAY DIFFRACTION | 2 | ALLB34 - 552 | | | | |
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